HsaINT0000601 @ hg19
Intron Retention
Gene
ENSG00000107331 | ABCA2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:HGNC Symbol;Acc:32]
Coordinates
chr9:139917154-139917512:-
Coord C1 exon
chr9:139917393-139917512
Coord A exon
chr9:139917318-139917392
Coord C2 exon
chr9:139917154-139917317
Length
75 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
TGACATCCGCCATGGTGCAGGGT
3' ss Score
4.57
Exon sequences
Seq C1 exon
TCTGCCAGCCTTCTACACAGCGGCGCCCCTGACGTCTGCCGGCATCCTGCCTGTCATGCAATCGCTGTGCCCGGACGGCCAGCGAGACGAGTTCGGCTTCCTGCAGTACGCCAACTCCAC
Seq A exon
GTGAGTGCCCACCCGCCCCTCGGAGCACCCACCCCTCCCCAGCCCATCCAGTGAGTGACATCCGCCATGGTGCAG
Seq C2 exon
GGTCACGCAGCTGCTTGAGCGCCTGGACCGCGTGGTGGAGGAAGGCAACCTGTTTGACCCAGCGCGGCCCAGCCTGGGCTCAGAGCTCGAGGCCCTACGCCAGCATCTGGAGGCCCTCAGTGCGGGCCCGGGCACCTCGGGGAGCCACCTGGACAGATCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107331-ABCA2:NM_001606:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.089
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCAGCCTTCTACACAGC
R:
TGGGTCAAACAGGTTGCCTTC
Band lengths:
180-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)